core: molecule: make Molecule::clone() accepting const reference to source molecule

**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**
As we are just cloning the Molecule, it should not require non-constant access to it (which could lead to unexpected side effects).

**Describe alternatives you've considered**
Making `Molecule::clone` const we ensure that nothing unexpected happens to source molecule.